library(tidyverse)
library(ggplot2)
library(rtracklayer)
library(AnnotationDbi)
library(EnsDb.Hsapiens.v86)
library(edgeR)
library(ggrepel)
load("~/mccoyLab/collabs/doubleseq_2021/code/batch_correct/combatseq_corrected_withshrinkage.RData")
#Importing metadata to differentiate between pregnant and not pregnant and other main covariates
meta <- read.csv("~/mccoyLab/collabs/doubleseq_2021/tidied_meta/tidied_meta_CREATE_kw_20220308.csv", row.names = 1) %>%
as.data.frame() %>%
mutate(across(c("cDNA_RT_Date", "Library_Prep_Date", "Sequencing_Date", "Study_Participant_ID"), as.factor))
#subsetting meta data to just the samples with sequencing data
remove <- setdiff(rownames(meta), colnames(corrected_jg_rts))
if (length(which(rownames(meta) %in% remove)) > 0){
meta <- meta[-which(rownames(meta) %in% remove),]
}
remove
## [1] "66-D-3-L" "93-A-1-L" "109-B-7-L" "127-A-1-L" "144-A-3-L"
## [6] "154-A-1-L" "155-A-16-L" "169-A-2-L" "197-A-3-L"
counts_order <- order(colnames(corrected_jg_rts))
meta_order <- order(rownames(meta))
counts <- corrected_jg_rts[, counts_order]
meta <- meta[meta_order, ]
meta$name <- rownames(meta)
counts_filter <- counts[rowMeans(counts) > 7.63295995515296,]
logged_cf <- log2(counts_filter + 1) %>% as.data.frame()
data_long_logged_cf <- logged_cf %>%
pivot_longer(colnames(logged_cf)) %>%
as.data.frame()
with_batch_lcf <- left_join(data_long_logged_cf, meta[,c("name", "cDNA_RT_Date", "Sequencing_Date", "Pregnant")], by="name")
ggplot(data_long_logged_cf, aes(x=value, col=name)) + geom_density(alpha=0.2) + theme_bw() + theme(legend.position = "none", panel.background = element_blank(), panel.grid = element_blank())

ggplot(with_batch_lcf, aes(x=value, group_by = name, col=as.factor(Pregnant))) + geom_density(alpha=0.2) + theme_bw() + theme(panel.background = element_blank(), panel.grid = element_blank())

ggplot(with_batch_lcf, aes(x=value, group_by = name, col=as.factor(Pregnant))) + geom_density(alpha=0.2) + theme_bw() + theme(panel.background = element_blank(), panel.grid = element_blank()) + facet_wrap(~cDNA_RT_Date)

ggplot(with_batch_lcf, aes(x=value, group_by = name, col=as.factor(Pregnant))) + geom_density(alpha=0.2) + theme_bw() + theme(panel.background = element_blank(), panel.grid = element_blank()) + facet_wrap(~Sequencing_Date)

pca_res_cf <- prcomp(t(counts_filter))
var_explained_cf <- pca_res_cf$sdev^2/sum(pca_res_cf$sdev^2)
pca_res_cf$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Sequencing_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_cf[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_cf[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_cf$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=meta$Sequencing_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_cf[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_cf[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_cf$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$cDNA_RT_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_cf[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_cf[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_cf$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=meta$cDNA_RT_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_cf[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_cf[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_cf$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Pregnant))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_cf[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_cf[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_cf$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=as.factor(meta$Pregnant))) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_cf[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_cf[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

file_gencode <- "~/genomes/hg38_genome/gencode.v34.annotation.gtf"
gtf <- rtracklayer::import(file_gencode) %>%
as.data.frame() %>%
dplyr::filter(type == "gene") %>%
dplyr::select(gene_id, seqnames, width) %>%
dplyr::rename(ensembl_gene_id = gene_id) %>%
dplyr::rename(chromosome_name = seqnames) %>%
dplyr::rename(length = width)
gene_table <- gtf[match(rownames(counts_filter), gtf$ensembl_gene_id),]
dgeFullData <- DGEList(counts_filter)
#normalize counts by TMM
TMMFullData <- calcNormFactors(dgeFullData, method="TMM")
TMMCounts <- as.matrix(TMMFullData$counts)
#TPM Calculation
calc_tpm <- function(x, gene.length) {
x <- as.matrix(x)
len.norm.lib.size <- colSums(x / gene.length)
return((t(t(x) / len.norm.lib.size) * 1e06)/ gene.length)
}
#creates a matrix with calculated TPM values for each sample from TMM normalized counts and the gene lengths
rawTPMvals <- calc_tpm(TMMFullData, gene.length = gene_table$length)
pca_res_tmm <- prcomp(t(TMMCounts))
var_explained_tmm <- pca_res_tmm$sdev^2/sum(pca_res_tmm$sdev^2)
pca_res_tpm <- prcomp(t(rawTPMvals))
var_explained_tpm <- pca_res_tpm$sdev^2/sum(pca_res_tpm$sdev^2)
pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Sequencing_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=meta$Sequencing_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_tmm[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$cDNA_RT_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=meta$cDNA_RT_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_tmm[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Pregnant))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=as.factor(meta$Pregnant))) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_tmm[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Sequencing_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=meta$Sequencing_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_tpm[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$cDNA_RT_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=meta$cDNA_RT_Date)) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_tpm[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Pregnant))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=as.factor(meta$Pregnant))) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_tpm[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

tmmsum <- colSums(TMMCounts)
rawsum <- colSums(counts_filter)
pca_res_cf$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=rawsum)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_cf[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_cf[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_cf$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=rawsum)) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_cf[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_cf[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=tmmsum)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC2, x=PC3, color=tmmsum)) +
geom_point() + theme_bw() +
labs(y=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%"),
x=paste0("PC3: ", round(var_explained_tmm[3]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.integer(meta$Study_Participant_ID))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$lining_thickness_mm)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Oocyte_Age)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Uterus_Age)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Sperm_Age)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Embryo_grade_at_freezing))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, label=rownames(meta))) +
geom_point() +
geom_text_repel() +
theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(panel.background = element_blank(), panel.grid = element_blank())

oi1 <- "163-A-1-L"
oi1i <- which(rownames(meta) == oi1)
oi2 <- "205-A-5-L"
oi2i <- which(rownames(meta) == oi2)
coloi <- rep(0, length(rownames(meta)))
coloi[c(oi1i, oi2i)] <- 1
pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color = as.factor(coloi), label=rownames(meta))) +
geom_point() +
geom_text_repel() +
theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(panel.background = element_blank(), panel.grid = element_blank())

sample_vec <- c("101-A-10-L", "103-A-4-L","104-A-8-L", "107-C-3-L","108-A-3-L", "11-B-12-L", "122-A-4-L", "125-A-4-L", "129-A-3-L", "130-A-13-L", "15-C-4-L", "152-A-5-L", "156-A-2-L", "167-C-4-L", "173-B-5-L",
"179-A-6-L", "180-A-1-L", "185-A-2-L", "2-A-3-L", "202-A-11-L","218-A-5-L",
"31-A-1-L","36-A-2-L", "37-A-4-L","4-B-1-L",
"54-A-10-L","59-B-6-L", "73-A-2-L","75-A-4-L", "88-A-7-L","89-A-2-L", "99-A-3-L" )
oii <- which(rownames(meta) %in% sample_vec)
coloi <- rep(0, length(rownames(meta)))
coloi[oii] <- 1
pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color = as.factor(coloi), label=rownames(meta))) +
geom_point() +
geom_text_repel() +
theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(panel.background = element_blank(), panel.grid = element_blank())
## Warning: ggrepel: 140 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$AOD)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$GC)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$BMI)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Infertility_type)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Previous_pregnancy)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Past_surgical_hist)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$FSH_D3)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$AMH)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$AFC)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$LH)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$E2_Day_2_3)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Type_of_trigger))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Total_Gn)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$E2_on_trigger)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Num_eggs)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Num_MII)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Time_to_stripping_hr)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Time_to_ICSI_hr)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Time_to_Biopsy_hr)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Interpretation)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Natural_cycle))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Medication))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Prednisone))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Fragmin))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$EG))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$HCG))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$IL))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$GCSF))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Metformin))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PRP))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Sildenafil))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Transferring_physician))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Transfer_catheter_used))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_SSM_GC))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_Egg_factor))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_MF))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_Uterine_factor))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_TF))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_RPL))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_RIF))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_Unexplained))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PMdH_none))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PMdH_vasculitis))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PMdH_immune))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PMdH_stress_hormones))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Ongoing_pregnancy))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tmm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Final_outcome))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tmm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tmm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.integer(meta$Study_Participant_ID))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$lining_thickness_mm)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Oocyte_Age)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Uterus_Age)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Sperm_Age)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Embryo_grade_at_freezing)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, label=rownames(meta))) +
geom_point() +
geom_text_repel() +
theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(panel.background = element_blank(), panel.grid = element_blank())

oi1 <- "163-A-1-L"
oi1i <- which(rownames(meta) == oi1)
oi2 <- "205-A-5-L"
oi2i <- which(rownames(meta) == oi2)
coloi <- rep(0, length(rownames(meta)))
coloi[c(oi1i, oi2i)] <- 1
pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color = as.factor(coloi), label=rownames(meta))) +
geom_point() +
geom_text_repel() +
theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(panel.background = element_blank(), panel.grid = element_blank())

oii <- which(rownames(meta) %in% sample_vec)
coloi <- rep(0, length(rownames(meta)))
coloi[oii] <- 1
pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color = as.factor(coloi), label=rownames(meta))) +
geom_point() +
geom_text_repel() +
theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(panel.background = element_blank(), panel.grid = element_blank())
## Warning: ggrepel: 130 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$AOD)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$GC)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$BMI)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Infertility_type)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Previous_pregnancy)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Past_surgical_hist)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$FSH_D3)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$AMH)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$AFC)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$LH)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$E2_Day_2_3)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Type_of_trigger))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Total_Gn)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$E2_on_trigger)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Num_eggs)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Num_MII)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Time_to_stripping_hr)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Time_to_ICSI_hr)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Time_to_Biopsy_hr)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=meta$Interpretation)) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Natural_cycle))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Medication))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Prednisone))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Fragmin))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$EG))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$HCG))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$IL))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$GCSF))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Metformin))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PRP))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Sildenafil))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Transferring_physician))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Transfer_catheter_used))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_SSM_GC))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_Egg_factor))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_MF))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_Uterine_factor))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_TF))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_RPL))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_RIF))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$InfD_Unexplained))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PMdH_none))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PMdH_vasculitis))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PMdH_immune))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$PMdH_stress_hormones))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Ongoing_pregnancy))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())

pca_res_tpm$x %>%
as.data.frame %>%
ggplot(aes(y=PC1, x=PC2, color=as.factor(meta$Final_outcome))) +
geom_point() + theme_bw() +
labs(y=paste0("PC1: ", round(var_explained_tpm[1]*100,1), "%"),
x=paste0("PC2: ", round(var_explained_tpm[2]*100,1), "%")) +
theme(legend.position = "top", panel.background = element_blank(), panel.grid = element_blank())
